Ask and you shall receive!
I am pretty sure rendering through the command line ignores the CUDA/OpenCL GPU rendering from the user-config, and for a few reasons. One, cycles rendering is actually an addon, and not built-in to Blender core 2.6. Because of this I am fairly positive that the GPU rendering feature itself is initialized when the UI is started, and something not required by the CLI rendering command. Because of this you’ll find the CLI GPU options for OpenGL (i.e. GPU debug).
Even so, there are always ways to push the process directly to the GPU, but to receive the same CUDA performance is a whole other thing. I am not sure what today’s nVidia Linux drivers provide (assuming that is what is even being used on that system), but it’s worth checking out.
To make find absolute answers, make sure that your BLENDER_USER_CONFIG environment variable is in fact pointing to the same directory as your Blender config, and turn on all of the debug/verbose options with your render command. You should at the very least see what Blender sees, and doesn’t like, or doesn’t support.
Best of luck!
